Bruker AVANCE User s Guide for the UWChemMRF by CG by guy22

VIEWS: 53 PAGES: 5

									Bruker AVANCE-360 User’s Guide
        for the UWChemMRF


                  by




                CG Fry




        last revised: 2004.08.01
Bruker Avance360 – Introduction                                                                                                   Page 2



                          UWChemMRF User Guide for XwinNMR


  I.         Introduction................................................................................................................ 3
        a)      Account information .............................................................................................. 3
        b)      Help........................................................................................................................ 3
        c)      Natoth SGI Unix – brief intro ................................................................................ 3
        d)      File structures and naming conventions................................................................. 4
        e)      XwinNMR and setres............................................................................................. 4
        f)      Editors .................................................................................................................... 4
        g)      Modern High-Field Spectrometers ........................................................................ 4
        h)      Starting and Stopping Acquisitions ....................................................................... 5
        i)      Plotting Data .......................................................................................................... 5

  II.        1H Acquisition—Example Session............................................................................ 6
        a)      Brief summary of commands................................................................................. 6
        b)      Detailed Setup........................................................................................................ 6

  III.          X-Nucleus Acquisitions—Example Session........................................................ 13
        a)      General Theme for X-Acquisitions...................................................................... 13
        b)      Detailed Setup for X-Acquisitions....................................................................... 13

  IV.           2D NMR on the AVANCE Spectrometer............................................................ 18
        a)      The Philosophy Used to Setup 2D Exps on the AVANCE-360 .......................... 18
        b)      COSY 2D Experiments........................................................................................ 18
        c)      HSQC 2D Experiments........................................................................................ 19
        d)      HMBC 2D Experiments....................................................................................... 20
Bruker Avance360 – Introduction                                                          Page 3




I. Introduction
   a) Account information
       •   passwd rules
           – do not use your email or 9th floor password; should be unique to CIC
           – use seven to eight characters, at least one non-alphanumeric
           – do not use any characters other than letters (case-sensitive), numbers,
              period, hyphen, underline
           – avoid simple substitutions: e.g., b00tleg is not a good password
       •   checkout requirements
           – all homework must be completed with 100% score before taking checkout
           – account locked-out one month after training if checkout not completed
           – account sharing will cause loss of access

   b) Help
       •   See “The Interaction Between XwinNMR and Unix,” pg. 4, 63 and 64
       •   All the Bruker manuals are accessible at the spectrometer under the XwinNMR
           Help menu.
       •   All the Bruker manuals are accessible on-line from our home page:
           go to:      http://cic.chem.wisc.edu/nmr/main.html
           find:       User Guides
           click on:   Bruker AVANCE User Guides
       •   These documents are available in the same area of the web site.

       Use the on-line and printed help manuals often and regularly. Asking questions
       prior to your having looked first yourself will not be well-tolerated.

   c) Natoth SGI Unix – brief intro
       •   See “The Interaction Between XwinNMR and Unix,” Part I; especially pgs. 5-7,
           15-18, and 27-30 (note: much of the rest requires root privileges)
       •   .cshrc and aliases
           dir                    ; ls –laF        (at UNIX prompt only; different in Xwin)
           df –k                  ; check disk utilization
           cd                     ; standard csh—puts in home directory
           cddata                 ; only cd alias that is user specific               pg 79-80
           cdshims                ; shims directory                                       pg 70
           cdpp                   ; pulse programs                                        pg 71
           cdpar                  ; parameter files                                  pgs 69, 84
           cdmac                  ; macros (simple command execution)                 pg 70, 90
           cdau                   ; automation files (c-like)                     pg 69, 85-89
           cdgp                   ; gradient programs                        missing on pg 69
Bruker Avance360 – Introduction                                                              Page 4


   d) File structures and naming conventions
       •   See “The Interaction Between XwinNMR and Unix,” Part II; pgs 66, 69, 70
       Filenames                                                14 letter limitation; edc
       Data locations and structure                                            pgs 79-80
       Shim files                                                                  pg 70
       Parameter files                                                        pgs 69, 84
       Pulse programs                                                              pg 71
       Macro files                                                            pgs 70, 90
       Automation files                                                    pgs 69, 85-89

   e) XwinNMR and setres
       •   See “The Interaction Between XwinNMR and Unix,” Part II; pg 91
       ZGSafety                   ; ‘yes’ initially, but must be set ‘no’ for multizg
       Default Editor             ; use “jot”
       XwinNMR                    ; set to “Extended”
       Apply                      ; will correct color/display problems

   f) Editors
       •   See “The Interaction Between XwinNMR and Unix,” pg. 72, 79
       edc                                             ; edit current (for new data acquistion)
       eda                                             ; edit acquisition parameters
       ased                                            ; automation setup editor (pp dependent)
       setti (edti; UW macro; also edinfo)             ; edit title (useful for data commenting)
       edte                                            ; edit temperature (temp panel)
       edhead                                          ; edit probehead (for probe changes)
       edp                                             ; edit processing parameters
       edg                                             ; edit plotting parameters

   g) Modern High-Field Spectrometers
       Linear Amplifiers     ; see edacb
          Bruker (stated in attenuation, not power!!)                                       Varian
           -6dB          high power proton bb probes                                          63
            0dB          high power X                                                         58
           ≤30dB         presaturation                                                        24
           ≤40dB         homodecoupling                                                       18
           ≤16dB         highpower decoupling                                                 41
           ≤10dB         highpower spinlock (check for update before using)                   41

       Tuning probes              ; see Acquisition Manual 1.5.4, pg A-60
           wobb                   ; needed for changes in temp for 1H
                                  ; required for all X-nucleus experiments
           wob                    ; UW macro, does an acqu prior to wobb
Bruker Avance360 – Introduction                                                    Page 5


   h) Starting and Stopping Acquisitions
       •   See “XwinNMR Acquisition Manual,” Section 1.7
       •   do not use quicknmr or run (they are not setup)
           zg          ; zero data then go
           go          ; do not zero data (ie., add to current)
           tr          ; transfer data for processing
           halt        ; preferred method for ending acquisition
           stop        ; immediate termination of acquisition, not as safe as halt
           suspend     ; suspend and resume only if pulse program supports (usually not)
           resume      ; resume only if supported in pulse program
           kill        ; will terminate active processes (e.g.,

   i) Plotting Data
       •   See “XwinPLOT manual” on cic website
       •   PLOT   button works fine in XwinNMR (but pretty limited)
       •   type xwinplot to start up very nice plot editor
           –   main customization is right-click on object and select 1D-2D-edit

								
To top